Genome-wide identification of AGO, DCL and RDR gene families and functional analysis of TdAGO30 under salt stress in wild emmer wheat

MicroRNA (miRNA) is a class of the endogenes negative regulator in plant, playing the pivotal role in numerous growth and developmental processes as well as diverse stress responses. Although the miRNA biosynthesis-related gene have been widely recognized across various plants, its significance is poorly understanded in wild emmer wheat (Tritum dicoccoides), particularly those involving in salt stress tolerance. In this study, 96 miRNA-related genes were obtained through a genome-wide search, including 54 AGOs (Argonautes), 29 DCLs (Dicer-likes) and 13 RDR (RNA-Dependent RNA Polymerases), respectively. Collinearity analysis revealed that polyploidization contributed to their expansion in wild emmer Additionally, analysis of genetic variations revealed a significant genetic bottleneck on them during the domestication of tetraploid wheat. Furthermore, 22 salt-responsive candidates were identified by expression pattern analysis. Integrated co-expression network and genome-wide association studies analysis(GWAS), TdAGO30 was found as a key genes involving in salt response. Finally, functional verification and RNA-seq analysis demonstrated that TdAGO30 negatively regulated salt tolerance by mediating osmotic regulation, hormone synthesis and ion transport. This study provided the useful information on the roles of miRNA-related genes in regulating salt tolerance in wild emmer wheat, which will contribute to improve salt tolerance through miRNA manipulation in wheat and other crops.